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added snakemake workflow for experiment
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JohannesGawron committed Jun 4, 2024
1 parent 6ff6f09 commit 6cc4408
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5 changes: 4 additions & 1 deletion .gitignore
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Rcode/markdowns/*
Rcode/*.html
!Rcode/markdowns/template.Rmd
workflow/.snakemake
experiments/.snakemake/*
.Rapp.history
*.Rhistory
experiments/data/markdowns/
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# Snakemake workflow for full reproducibility of the project

## Description
## Usage
Run
`snakemake --configfile config/config.yaml --cores 4 --use-conda`


To run the workflow, run `snakemake`

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above).

Owner: Johannes Gawron
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repos:
- repo: https://github.com/snakemake/snakefmt
rev: v0.10.2 # Replace by any tag/version ≥0.2.4 : https://github.com/snakemake/snakefmt/releases
hooks:
- id: snakefmt
2 changes: 2 additions & 0 deletions experiments/config/config.yaml
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sample: ['Br11', 'Br7', 'Br61', 'Br38', 'LM2', 'Pr9', 'Br23','Br39', 'Br57', 'Lu2', 'Br16_AC', 'Br16_B', 'Br16_C', 'Br26', 'Br44', 'Lu7', 'Br30', 'Br45', 'Ov8', 'Br37', 'Br46', 'Brx50', 'Pr6']
author: Johannes Gawron
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from pathlib import Path

SAMPLES = config['sample']
PROJECT_DIR = Path(workflow.basedir).parent
SCRIPT_DIR = Path(workflow.basedir) / 'scripts'
RESOURCES_DIR = Path(workflow.basedir) / 'resources'
markdown_helper_functions = (RESOURCES_DIR / 'functions.R').resolve().as_posix().replace('/', '\\/')
print(markdown_helper_functions)

######Rules######
include: 'rules/base.smk'



all_files = []
for sample in SAMPLES:
all_files.append((PROJECT_DIR / 'data' / 'htmls' / f'{sample}.html').resolve())


rule all:
input:
all_files
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channels:
- conda-forge
- bioconda
- r
- defaults
dependencies:
- r>=4.3
- r-rcpp>=1.0
- r-tidyverse>=2.0
- pandoc>=3.1
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